Nucleic acid metabolism

DNA metabolism

Replication, repair, and recombination—the three main processes of DNA metabolism—are carried out by specialized machinery within the cell. DNA must be replicated accurately in order to ensure the integrity of the genetic code. Errors that creep in during replication or because of damage after replication must be repaired. Finally, recombination between genomes is an important mechanism to provide variation within a species and to assist the repair of damaged DNA. The details of each process have been worked out in prokaryotes, where the machinery is more streamlined, simpler, and more amenable to study. Many of the basic principles appear to be similar in eukaryotes.

Basic mechanisms

DNA replication is a semiconservative process in which the two strands are separated and new complementary strands are generated independently, resulting in two exact copies of the original DNA molecule. Each copy thus contains one strand that is derived from the parent and one newly synthesized strand. Replication begins at a specific point on a chromosome called an origin, proceeds in both directions along the strand, and ends at a precise point. In the case of circular chromosomes, the end is reached automatically when the two extending chains meet, at which point specific proteins join the strands. DNA polymerases cannot initiate replication at the end of a DNA strand; they can only extend preexisting oligonucleotide fragments called primers. Therefore, in linear chromosomes, special mechanisms initiate and terminate DNA synthesis to avoid loss of information. The initiation of DNA synthesis is usually preceded by synthesis of a short RNA primer by a specialized RNA polymerase called primase. Following DNA replication, the initiating primer RNAs are degraded.

The two DNA strands are replicated in different fashions dictated by the direction of the phosphodiester bond. The leading strand is replicated continuously by adding individual nucleotides to the 3′ end of the chain. The lagging strand is synthesized in a discontinuous manner by laying down short RNA primers and then filling the gaps by DNA polymerase, such that the bases are always added in the 5′ to 3′ direction. The short RNA fragments made during the copying of the lagging strand are degraded when no longer needed. The two newly synthesized DNA segments are joined by an enzyme called DNA ligase. In this way, replication can proceed in both directions, with two leading strands and two lagging strands proceeding outward from the origin.

DNA polymerase adds single nucleotides to the 3′ end of either an RNA or a DNA molecule. In the prokaryote E. coli, there are three DNA polymerases; one is responsible for chromosome replication, and the other two are involved in the resynthesis of DNA during damage repair. DNA polymerases of eukaryotes are even more complicated. In human cells, for instance, more than five different DNA polymerases have been characterized. Separate polymerases catalyze the synthesis of the leading and lagging strands in human cells, and a separate polymerase is responsible for replication of mitochondrial DNA. The other polymerases are involved in the repair of DNA damage.

A number of other proteins are also essential for replication. Proteins called DNA helicases help to separate the two strands of DNA, and single-stranded DNA binding proteins stabilize them during opening prior to being copied. The opening of the DNA helix introduces considerable strain in the form of supercoiling, a movement that is subsequently relaxed by enzymes called topoisomerases (see aboveSupercoiling). A special RNA polymerase called primase synthesizes the primers needed at the origin to begin transcription, and DNA ligase seals the nicks formed between individual fragments.

The ends of linear eukaryotic chromosomes are marked by special sequences called telomeres that are synthesized by a special DNA polymerase called telomerase. This enzyme contains an RNA component that serves as a template for the exact sequence found at the ends of chromosomes. Multiple copies of a short sequence within the telomerase-associated RNA are made and added to the telomere ends. This has the effect of preventing shortening of the DNA chain that would otherwise occur during replication.

Single-stranded viral genomes, mitochondrial genomes, and some viral genomes are replicated in specialized ways. Several viruses such as adenovirus use a nucleotide covalently bound to a protein as a primer, and the protein remains covalently bound to the DNA after replication. Many single-stranded viruses use a rolling circle mechanism of replication whereby a double-stranded copy of the virus is first made. The replicating machinery then copies the nonviral strand in a continuous fashion, generating long single-stranded DNA from which full-length viral DNA strands are excised by specialized nucleases.

Recombination is the principal mechanism through which variation is introduced into populations. For example, during meiosis, the process that produces sex cells (sperm or eggs), homologous chromosomes—one derived from the mother and the equivalent from the father—become paired, and recombination, or crossing-over, takes place. The two DNA molecules are fragmented, and similar segments of the chromosome are shuffled to produce two new chromosomes, each being a mosaic of the originals. The pair separates so that each sperm or egg receives just one of the shuffled chromosomes. When sperm and egg fuse, the normal set of two copies of each chromosome is restored.

There are two forms of recombination, general and site-specific. General recombination typically involves cleavage and rejoining at identical or very similar sequences. In site-specific recombination, cleavage takes place at a specific site into which DNA is usually inserted. General recombination occurs among viruses during infection, in bacteria during conjugation, during transformation whereby DNA is directly introduced into cells, and during some types of repair processes. Site-specific recombination is frequently involved in the parasitic distribution of DNA segments throughout genomes. Many viruses, as well as special segments of DNA called transposons, rely on site-specific recombination to multiply and spread. The two processes are described in greater detail below.

General recombination, also called homologous recombination, involves two DNA molecules that have long stretches of similar base sequences. The DNA molecules are nicked to produce single strands; these subsequently invade the other duplex, where base pairing leads to a four-stranded DNA structure. The cruciform junction within this structure is called a Holliday junction, named after Robin Holliday, who proposed the original model for homologous recombination in 1964. The Holliday junction travels along the DNA duplex by “unzipping” one strand and reforming the hydrogen bonds on the second strand. Following this branch migration, the two duplexes can be nicked again, allowing them to separate. Finally, the nicks are repaired by DNA ligase. The result is two DNA duplexes in which the segment between the two nicks has been replaced. The enzymes involved in recombination have been characterized best in the prokaryote E. coli. A key enzyme is RecA, which catalyzes the strand invasion process. RecA coats single-stranded DNA and facilitates its pairing with a double-stranded DNA molecule containing the same sequence, which produces a loop structure.

Another protein, known as RecBC, is important for the recombination process. Functioning at free ends of DNA, RecBC catalyzes an unwinding-rewinding reaction as it traverses the length of the molecule. Since unwinding is faster than rewinding, a loop is produced behind the enzyme that facilitates subsequent pairing with another DNA molecule. A number of other proteins are also important for recombination, including single-stranded DNA binding proteins that stabilize single-stranded DNA, DNA polymerase to repair any gaps that might be formed, and DNA ligase to reseal the nicks after recombination is complete. The details of eukaryotic recombination are expected to parallel those found in E. coli, although the highly compact chromatin structure in eukaryotes makes the process more complicated.

It is important to note that the initial product of recombination between two regions of DNA that are similar but not identical will be a “heteroduplex”—that is, a molecule in which mismatched bases will be present at some positions in the helix. Thus, in the specialized recombination that takes place during meiosis, one round of replication is necessary before the mosaic chromosomes produced by recombination are properly matched. Enzymes are present in cells that specifically recognize and repair mismatches, so that the initial products of recombination can sometimes be repaired before they are replicated. In such cases the final products of replication will not be true reciprocal events, but rather one of the original parental molecules will appear to have been maintained to the exclusion of the other—a process called gene conversion.

Recombination also functions occasionally to repair lesions in DNA. If one chromosome of a pair becomes irreversibly damaged, the information from the other chromosome can be copied and inserted by recombination to provide a correct replacement of the damaged section. The key idea here is that sequences flanking the damage from a sister chromosome can base-pair with the corresponding sequences on the damaged chromosome, thus allowing replication to copy the correct sequence and repair the lesion.

Site-specific recombination

Site-specific recombination involves very short specific sequences that are recognized by proteins. Long DNA sequences such as viral genomes, drug-resistance elements, and regulatory sequences such as the mating type locus in yeast can be inserted, removed, or inverted, having profound regulatory effects. More than any other mechanism, site-specific recombination is responsible for reshaping genomes. For example, the genomes of many higher organisms, including plants and humans, show evidence that transposable elements have been constantly inserted throughout the genome and even into one another from time to time.

One example of site-specific recombination is the integration of DNA from bacteriophage λ into the chromosome of E. coli. In this reaction, bacteriophage λ DNA, which is a linear molecule in the normal phage, first forms a circle and then is cleaved by the enzyme λ-integrase at a specific site called the phage attachment site. A similar site on the bacterial chromosome is cut by integrase to give ends with the identical extension. Because of the complementarity between these two ends, they can be rejoined so that the original circular λ chromosome is inserted into the chromosome of the E. coli bacterium. Once integrated, the phage can be held in an inactive state until signals are generated that reverse the process, allowing the phage genome to escape and resume its normal life cycle of growth and spread into other bacteria. This site-specific recombination process requires only λ-integrase and one host DNA binding protein called the integration host factor. A third protein, called excisionase, recognizes the hybrid sites formed on integration and, in conjunction with integrase, catalyzes an excision process whereby the λ chromosome is removed from the bacterial chromosome.

A similar but more widespread version of DNA integration and excision is exhibited by the transposons, the so-called jumping genes. These elements range in size from fewer than 1,000 to as many as 40,000 base pairs. Transposons are able to move from one location in a genome to another, as first discovered in corn (maize) during the 1940s and ’50s by Barbara McClintock, whose work won her a Nobel Prize in 1983. Most, if not all, transposons encode an enzyme called transposase that acts much like λ-integrase by cleaving the ends of the transposon as well as its target site. Transposons differ from bacteriophage λ in that they do not have a separate existence outside of the chromosome but rather are always maintained in an integrated site. Two types of transposition can occur—one in which the element simply moves from one site in the chromosome to another and a second in which the transposon is replicated prior to moving. This second type of transposition leaves behind the original copy of the transposon and generates a second copy that is inserted elsewhere in the genome. Known as replicative transposition, this process is the mechanism responsible for the vast spread of transposable elements in many higher organisms.

The simplest kinds of transposons merely contain a copy of the transposase with no additional genes. They behave as parasitic elements and usually have no known associated function that is advantageous to the host. More often, transposable elements have additional genes associated with them—for example, antibiotic resistance factors. Antibiotic resistance typically occurs when an infecting bacterium acquires a plasmid that carries a gene encoding resistance to one or more antibiotics. Typically, these resistance genes are carried on transposable elements that have moved into plasmids and are easily transferred from one organism to another. Once a bacterium picks up such a gene, it enjoys a great selective advantage because it can grow in the presence of the antibiotic. Indiscriminate use of antibiotics actually promotes the buildup of these drug-resistant plasmids and strains.

It is extremely important that the integrity of DNA be maintained in order to ensure the accurate workings of a cell over its lifetime and to make certain that genetic information is accurately passed from one generation to the next. This maintenance is achieved by repair processes that constantly monitor the DNA for lesions and activate appropriate repair enzymes. As described in the section General recombination, serious lesions in DNA such as pyrimidine dimers or gaps can be repaired by recombination mechanisms, but there are many other repair mechanisms.

One important mechanism is that of mismatch repair, which has been studied extensively in E. coli. The system is directed by the presence of a methyl group within the sequence GATC on the template strand. Comparable systems for mismatch repair also operate in eukaryotes, though the template strand is not marked by methyl groups. In fact, lesions within the genes for human mismatch repair systems are known to be responsible for many cancers. Loss of the mismatch repair system allows mutations to build up quickly and eventually to affect the genes that cause cells to divide. As a result, cells divide in an uncontrolled manner and become cancerous.

Once replication is complete, the most common kind of damage to nucleic acids is one in which the normal A, C, G, and T bases are changed into chemically modified bases that usually differ significantly from their natural counterparts. The only exceptions are the deamination of cytosine to uracil and the deamination of 5-methylcytosine to thymine. In these cases the product is a G:U or G:T mismatch. Specific enzymes called DNA glycosylases can recognize uracil in DNA or the thymine in a G:T mismatch and can selectively remove the base by cleaving the bond between the base and the deoxyribosesugar. Many of these enzymes are specific for the different chemically modified bases that may be present in DNA.

Another common means of repairing DNA lesions is by an excision repair pathway. Enzymes recognize damage within DNA, probably by detecting an altered conformation of DNA, and then nick the strand on either side of the lesion, allowing a small single-stranded DNA to be excised. DNA polymerase and DNA ligase then repair the single-stranded gap. In all of these systems, the presence of an abnormal base signifies which strand is to be repaired, and the complementary strand is used as the template to ensure the accuracy of repair.

RNA metabolism

RNA provides the link between the genetic information encoded in DNA and the actual workings of the cell. Some RNA molecules such as the rRNAs and the snRNAs (described in the section Types of RNA) become part of complicated ribonucleoprotein structures with specialized roles in the cell. Others such as tRNAs play key roles in protein synthesis, while mRNAs direct the synthesis of proteins by the ribosome. Three distinct phases of RNA metabolism occur. First, selected segments of the genome are copied by transcription to produce the precursor RNAs. Second, these precursors are processed to become functionally mature RNAs ready for use. When these RNAs are mRNAs, they are then used for translation. Third, after use the RNAs are degraded, and the bases are recycled. Thus, transcription is the process where a specific segment of DNA, a gene, is copied into a specific RNA that encodes a single protein or plays a structural or catalytic role. Translation is the decoding of the information within mRNA molecules that takes place on a specialized structure called a ribosome. There are important differences in both transcription and translation between prokaryotic and eukaryotic organisms.

Small segments of DNA are transcribed into RNA by the enzyme RNA polymerase, which achieves this copying in a strictly controlled process. The first step is to recognize a specific sequence on DNA called a promoter that signifies the start of the gene. The two strands of DNA become separated at this point, and RNA polymerase begins copying from a specific point on one strand of the DNA using a ribonucleoside 5′-triphosphate to begin the growing chain. Additional ribonucleoside triphosphates are used as the substrate, and, by cleavage of their high-energy phosphate bond, ribonucleoside monophosphates are incorporated into the growing RNA chain. Each successive ribonucleotide is directed by the complementary base pairing rules of DNA. Thus, a C in DNA directs the incorporation of a G into RNA, G is copied into C, T into A, and A into U. Synthesis continues until a termination signal is reached, at which point the RNA polymerase drops off the DNA, and the RNA molecule is released. In some cases this RNA molecule is the final mRNA. In other cases it is a pre-mRNA and requires further processing before it is ready for translation by the ribosome. Ahead of many genes in prokaryotes, there are signals called “operators” where specialized proteins called repressors bind to the DNA just upstream of the start point of transcription and prevent access to the DNA by RNA polymerase. These repressor proteins thus prevent transcription of the gene by physically blocking the action of the RNA polymerase. Typically, repressors are released from their blocking action when they receive signals from other molecules in the cell indicating that the gene needs to be expressed. Ahead of some prokaryotic genes are signals to which activator proteins bind that positively induce transcription.

Transcription in higher organisms is more complicated. First, the RNA polymerase of eukaryotes is a more complicated enzyme than the relatively simple five-subunit enzyme of prokaryotes. In addition, there are many more accessory factors that help to control the efficiency of the individual promoters. These accessory proteins are called transcription factors and typically respond to signals from within the cell that indicate whether transcription is required. In many human genes, several transcription factors may be needed before transcription can proceed efficiently. A transcription factor can cause either repression or activation of gene expression in eukaryotes.

During transcription, only one strand of the DNA is usually copied. This is called the template strand, and the RNA molecules produced are single-stranded. The DNA strand that would correspond to the mRNA is called the coding or sense strand, and it is not unusual for this to change from one gene to the next. In eukaryotes the initial product of transcription is called a pre-mRNA, which is extensively spliced before the mature mRNA is produced, ready for translation by the ribosome.

Translation

The process of translation uses the information present in the nucleotide sequence of mRNA to direct the synthesis of a specific protein for use by the cell. Translation takes place on the ribosomes—complex particles in the cell that contain RNA and protein. In prokaryotes the ribosomes are loaded onto the mRNA while transcription is still ongoing. Near the 5′ end of the mRNA, a short sequence of nucleotides signals the starting point for translation. It contains a few nucleotides called a ribosome binding site, or Shine-Dalgarno sequence. In E. coli the tetranucleotide GAGG is sufficient to serve as a binding site. This typically lies five to eight bases upstream of an initiation codon. The mRNA sequence is read three bases at a time from its 5′ end toward its 3′ end, and one amino acid is added to the growing chain from its respective aminoacyl tRNA, until the complete protein chain is assembled. Translation stops when the ribosome encounters a termination codon, normally UAG, UAA, or UGA. Special release factors associate with the ribosome in response to these codons, and the newly synthesized protein, tRNAs, and mRNA all dissociate. The ribosome then becomes available to interact with another mRNA molecule.

In eukaryotes the essence of protein synthesis is the same, although the ribosomes are more complicated. As with prokaryotic initiation, the signal sequence interacts with the 3′ end of the small subunit rRNA during formation of the initiation complex.

The issue of fidelity is important during protein synthesis, but it is not as crucial as fidelity during replication. One mRNA molecule can be translated repeatedly to give many copies of the protein. When an occasional protein is mistranslated, it usually does not fold properly and is then degraded by the cellular machinery. However, proofreading mechanisms exist within the ribosome to ensure accurate pairing between the codon in the mRNA and the anticodon in the tRNA.

One of the crowning achievements of molecular biology was the elucidation during the 1960s of the genetic code. Principals in this effort were Har G. Khorana and Marshall W. Nirenberg, who shared a Nobel Prize in 1968. Khorana and Nirenberg used artificial templates and protein synthesizing systems in the test tube to determine the coding potential of all 64 possible triplet codons (see the table). The key feature of the genetic code is that the 20 amino acids are encoded by 61 codons. Thus, there is degeneracy in the code such that one amino acid is often specified by more than one codon. In the case of serine and leucine, six codons can be used for each. Among organisms that have been examined in detail, the code appears to be almost universal, from bacteria through archaea to eukaryotes. The known exceptions are found in the mitochondria of humans and many other organisms as well as in some species of bacteria. The structure within the genetic code whereby many amino acids are uniquely coded by the first two bases of the codon strongly suggests that the code has itself evolved from a more primitive code involving 16 dinucleotides. How the individual amino acids became associated with the different codons remains a matter of speculation.